Following your instructions and recreating your steps with FreeBSD 9 amd64 with three copied images on KVM, I was unable to recreate a scenario where the wheel group was removed from the system.

I know that's not helpful, but it means that something else is missing. If you can look through bash history or anything else to determine what else might have been done or changed, or if you can get a timestamp for when the wheel group was removed, it may help to shed light. Otherwise I can't pretend to know more.